Zinc in PDB 8c61: Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa
Protein crystallography data
The structure of Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa, PDB code: 8c61
was solved by
K.Wendrich,
M.Gersch,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
63.28 /
2.50
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
122.743,
126.559,
144.167,
90,
90,
90
|
R / Rfree (%)
|
20 /
24.3
|
Other elements in 8c61:
The structure of Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa also contains other interesting chemical elements:
Zinc Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Zinc atom in the Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa
(pdb code 8c61). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the
Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa, PDB code: 8c61:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Zinc binding site 1 out
of 12 in 8c61
Go back to
Zinc Binding Sites List in 8c61
Zinc binding site 1 out
of 12 in the Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn801
b:80.3
occ:1.00
|
NE2
|
A:HIS67
|
2.1
|
85.8
|
1.0
|
SG
|
A:CYS74
|
2.3
|
84.3
|
1.0
|
SG
|
A:CYS77
|
2.3
|
74.9
|
1.0
|
SG
|
A:CYS69
|
2.3
|
80.4
|
1.0
|
CE1
|
A:HIS67
|
3.0
|
85.0
|
1.0
|
CB
|
A:CYS69
|
3.1
|
85.3
|
1.0
|
CD2
|
A:HIS67
|
3.1
|
80.1
|
1.0
|
CB
|
A:CYS74
|
3.4
|
78.7
|
1.0
|
CB
|
A:CYS77
|
3.4
|
67.3
|
1.0
|
CA
|
A:CYS69
|
3.4
|
86.3
|
1.0
|
N
|
A:CYS77
|
3.8
|
65.6
|
1.0
|
CA
|
A:CYS77
|
4.1
|
70.1
|
1.0
|
N
|
A:MET70
|
4.1
|
81.0
|
1.0
|
ND1
|
A:HIS67
|
4.1
|
84.1
|
1.0
|
CG
|
A:HIS67
|
4.2
|
77.8
|
1.0
|
C
|
A:CYS69
|
4.3
|
91.7
|
1.0
|
N
|
A:CYS69
|
4.5
|
80.0
|
1.0
|
CB
|
A:PHE76
|
4.6
|
73.1
|
1.0
|
CA
|
A:CYS74
|
4.8
|
77.4
|
1.0
|
O
|
A:GLY71
|
4.8
|
102.0
|
1.0
|
C
|
A:PHE76
|
4.8
|
70.4
|
1.0
|
O
|
A:LYS68
|
5.0
|
79.9
|
1.0
|
|
Zinc binding site 2 out
of 12 in 8c61
Go back to
Zinc Binding Sites List in 8c61
Zinc binding site 2 out
of 12 in the Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn802
b:65.9
occ:1.00
|
ND1
|
A:HIS153
|
2.0
|
60.3
|
1.0
|
ND1
|
A:HIS133
|
2.0
|
62.1
|
1.0
|
SG
|
A:CYS150
|
2.3
|
63.9
|
1.0
|
SG
|
A:CYS145
|
2.3
|
72.5
|
1.0
|
CE1
|
A:HIS153
|
2.9
|
64.6
|
1.0
|
CE1
|
A:HIS133
|
3.0
|
63.1
|
1.0
|
CG
|
A:HIS133
|
3.0
|
65.8
|
1.0
|
CG
|
A:HIS153
|
3.1
|
63.5
|
1.0
|
CB
|
A:CYS145
|
3.2
|
73.1
|
1.0
|
CB
|
A:HIS133
|
3.3
|
60.1
|
1.0
|
CB
|
A:CYS150
|
3.3
|
70.5
|
1.0
|
CB
|
A:HIS153
|
3.5
|
50.7
|
1.0
|
NE2
|
A:HIS133
|
4.1
|
60.1
|
1.0
|
CA
|
A:HIS133
|
4.1
|
67.1
|
1.0
|
NE2
|
A:HIS153
|
4.1
|
71.0
|
1.0
|
CD2
|
A:HIS133
|
4.1
|
54.9
|
1.0
|
CD2
|
A:HIS153
|
4.2
|
58.4
|
1.0
|
CB
|
A:ALA137
|
4.2
|
67.4
|
1.0
|
N
|
A:HIS153
|
4.3
|
64.1
|
1.0
|
CA
|
A:HIS153
|
4.5
|
68.4
|
1.0
|
CA
|
A:CYS145
|
4.6
|
82.4
|
1.0
|
O
|
A:HIS133
|
4.7
|
71.0
|
1.0
|
CA
|
A:CYS150
|
4.8
|
76.8
|
1.0
|
C
|
A:HIS133
|
4.8
|
71.3
|
1.0
|
|
Zinc binding site 3 out
of 12 in 8c61
Go back to
Zinc Binding Sites List in 8c61
Zinc binding site 3 out
of 12 in the Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn803
b:81.4
occ:1.00
|
SG
|
A:CYS229
|
2.3
|
89.8
|
1.0
|
SG
|
A:CYS169
|
2.3
|
72.9
|
1.0
|
SG
|
A:CYS166
|
2.3
|
78.5
|
1.0
|
SG
|
A:CYS225
|
2.4
|
69.3
|
1.0
|
CB
|
A:CYS229
|
3.1
|
68.7
|
1.0
|
CB
|
A:CYS169
|
3.1
|
71.6
|
1.0
|
CB
|
A:CYS166
|
3.1
|
67.4
|
1.0
|
CB
|
A:CYS225
|
3.3
|
68.7
|
1.0
|
N
|
A:CYS169
|
3.8
|
76.3
|
1.0
|
CA
|
A:CYS169
|
4.0
|
77.0
|
1.0
|
OG
|
A:SER168
|
4.1
|
105.6
|
1.0
|
N
|
A:CYS229
|
4.1
|
75.8
|
1.0
|
CA
|
A:CYS229
|
4.2
|
83.3
|
1.0
|
CA
|
A:CYS166
|
4.6
|
77.1
|
1.0
|
CA
|
A:CYS225
|
4.6
|
71.0
|
1.0
|
CB
|
A:ALA171
|
4.6
|
69.0
|
1.0
|
C
|
A:CYS169
|
4.7
|
80.2
|
1.0
|
N
|
A:GLY170
|
4.9
|
76.4
|
1.0
|
N
|
A:ALA171
|
4.9
|
74.3
|
1.0
|
C
|
A:SER168
|
5.0
|
89.0
|
1.0
|
|
Zinc binding site 4 out
of 12 in 8c61
Go back to
Zinc Binding Sites List in 8c61
Zinc binding site 4 out
of 12 in the Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn801
b:122.1
occ:1.00
|
NE2
|
D:HIS67
|
2.0
|
123.6
|
1.0
|
SG
|
D:CYS77
|
2.3
|
135.9
|
1.0
|
SG
|
D:CYS69
|
2.3
|
140.3
|
1.0
|
SG
|
D:CYS74
|
2.3
|
129.9
|
1.0
|
CB
|
D:CYS69
|
3.0
|
128.8
|
1.0
|
CD2
|
D:HIS67
|
3.0
|
122.3
|
1.0
|
CE1
|
D:HIS67
|
3.0
|
116.9
|
1.0
|
CA
|
D:CYS69
|
3.2
|
127.2
|
1.0
|
CB
|
D:CYS77
|
3.3
|
116.3
|
1.0
|
CB
|
D:CYS74
|
3.3
|
134.5
|
1.0
|
N
|
D:CYS77
|
3.8
|
112.1
|
1.0
|
N
|
D:MET70
|
4.1
|
136.2
|
1.0
|
CA
|
D:CYS77
|
4.1
|
115.5
|
1.0
|
ND1
|
D:HIS67
|
4.1
|
121.8
|
1.0
|
CG
|
D:HIS67
|
4.1
|
118.0
|
1.0
|
C
|
D:CYS69
|
4.2
|
134.0
|
1.0
|
N
|
D:CYS69
|
4.3
|
128.6
|
1.0
|
CB
|
D:PHE76
|
4.5
|
113.9
|
1.0
|
CA
|
D:CYS74
|
4.8
|
133.6
|
1.0
|
N
|
D:GLY71
|
4.8
|
146.7
|
1.0
|
C
|
D:PHE76
|
4.8
|
119.2
|
1.0
|
|
Zinc binding site 5 out
of 12 in 8c61
Go back to
Zinc Binding Sites List in 8c61
Zinc binding site 5 out
of 12 in the Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn802
b:90.4
occ:1.00
|
ND1
|
D:HIS133
|
2.1
|
88.1
|
1.0
|
ND1
|
D:HIS153
|
2.1
|
95.7
|
1.0
|
SG
|
D:CYS150
|
2.3
|
95.6
|
1.0
|
SG
|
D:CYS145
|
2.3
|
109.4
|
1.0
|
CE1
|
D:HIS133
|
2.9
|
91.3
|
1.0
|
CE1
|
D:HIS153
|
3.0
|
93.3
|
1.0
|
CG
|
D:HIS153
|
3.1
|
89.7
|
1.0
|
CG
|
D:HIS133
|
3.1
|
94.1
|
1.0
|
CB
|
D:CYS145
|
3.3
|
104.6
|
1.0
|
CB
|
D:HIS153
|
3.4
|
89.6
|
1.0
|
CB
|
D:CYS150
|
3.5
|
104.7
|
1.0
|
CB
|
D:HIS133
|
3.5
|
97.7
|
1.0
|
NE2
|
D:HIS133
|
4.1
|
94.6
|
1.0
|
NE2
|
D:HIS153
|
4.1
|
87.0
|
1.0
|
CD2
|
D:HIS133
|
4.2
|
96.5
|
1.0
|
CD2
|
D:HIS153
|
4.2
|
90.5
|
1.0
|
CA
|
D:HIS133
|
4.3
|
103.6
|
1.0
|
N
|
D:HIS153
|
4.3
|
98.2
|
1.0
|
CA
|
D:HIS153
|
4.5
|
90.1
|
1.0
|
CA
|
D:CYS145
|
4.7
|
111.6
|
1.0
|
CA
|
D:CYS150
|
4.9
|
108.2
|
1.0
|
O
|
D:HIS133
|
5.0
|
120.4
|
1.0
|
|
Zinc binding site 6 out
of 12 in 8c61
Go back to
Zinc Binding Sites List in 8c61
Zinc binding site 6 out
of 12 in the Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn803
b:84.3
occ:1.00
|
SG
|
D:CYS166
|
2.3
|
89.4
|
1.0
|
SG
|
D:CYS229
|
2.3
|
94.1
|
1.0
|
SG
|
D:CYS225
|
2.3
|
89.1
|
1.0
|
SG
|
D:CYS169
|
2.4
|
88.7
|
1.0
|
CB
|
D:CYS166
|
3.2
|
85.5
|
1.0
|
CB
|
D:CYS225
|
3.2
|
90.6
|
1.0
|
CB
|
D:CYS229
|
3.2
|
91.0
|
1.0
|
CB
|
D:CYS169
|
3.4
|
90.6
|
1.0
|
N
|
D:CYS169
|
4.1
|
89.6
|
1.0
|
CA
|
D:CYS169
|
4.3
|
94.8
|
1.0
|
N
|
D:CYS229
|
4.3
|
89.0
|
1.0
|
CA
|
D:CYS229
|
4.4
|
85.0
|
1.0
|
CB
|
D:ALA171
|
4.5
|
90.5
|
1.0
|
CB
|
D:GLU231
|
4.5
|
95.2
|
1.0
|
CA
|
D:CYS225
|
4.6
|
92.2
|
1.0
|
CA
|
D:CYS166
|
4.6
|
88.7
|
1.0
|
C
|
D:CYS169
|
4.9
|
90.2
|
1.0
|
CG
|
D:GLU231
|
4.9
|
96.8
|
1.0
|
|
Zinc binding site 7 out
of 12 in 8c61
Go back to
Zinc Binding Sites List in 8c61
Zinc binding site 7 out
of 12 in the Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Zn801
b:77.2
occ:1.00
|
NE2
|
G:HIS67
|
2.1
|
75.0
|
1.0
|
SG
|
G:CYS69
|
2.3
|
81.8
|
1.0
|
SG
|
G:CYS77
|
2.3
|
77.5
|
1.0
|
SG
|
G:CYS74
|
2.3
|
85.4
|
1.0
|
CB
|
G:CYS69
|
2.9
|
73.3
|
1.0
|
CE1
|
G:HIS67
|
3.0
|
79.3
|
1.0
|
CD2
|
G:HIS67
|
3.2
|
79.8
|
1.0
|
CB
|
G:CYS74
|
3.2
|
89.2
|
1.0
|
CB
|
G:CYS77
|
3.3
|
77.4
|
1.0
|
CA
|
G:CYS69
|
3.4
|
85.0
|
1.0
|
N
|
G:CYS77
|
3.8
|
71.4
|
1.0
|
CA
|
G:CYS77
|
4.0
|
73.7
|
1.0
|
ND1
|
G:HIS67
|
4.2
|
78.5
|
1.0
|
N
|
G:MET70
|
4.2
|
87.5
|
1.0
|
C
|
G:CYS69
|
4.3
|
89.6
|
1.0
|
CG
|
G:HIS67
|
4.3
|
77.8
|
1.0
|
N
|
G:CYS69
|
4.4
|
81.9
|
1.0
|
CB
|
G:PHE76
|
4.5
|
64.2
|
1.0
|
CA
|
G:CYS74
|
4.7
|
92.0
|
1.0
|
C
|
G:PHE76
|
4.7
|
73.8
|
1.0
|
O
|
G:GLY71
|
4.8
|
107.9
|
1.0
|
CD1
|
G:PHE76
|
4.8
|
69.2
|
1.0
|
|
Zinc binding site 8 out
of 12 in 8c61
Go back to
Zinc Binding Sites List in 8c61
Zinc binding site 8 out
of 12 in the Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Zn802
b:65.5
occ:1.00
|
ND1
|
G:HIS153
|
2.0
|
61.7
|
1.0
|
ND1
|
G:HIS133
|
2.1
|
50.4
|
1.0
|
SG
|
G:CYS150
|
2.3
|
64.5
|
1.0
|
SG
|
G:CYS145
|
2.3
|
71.5
|
1.0
|
CE1
|
G:HIS133
|
2.9
|
63.7
|
1.0
|
CE1
|
G:HIS153
|
3.0
|
57.7
|
1.0
|
CG
|
G:HIS153
|
3.0
|
63.5
|
1.0
|
CG
|
G:HIS133
|
3.1
|
65.0
|
1.0
|
CB
|
G:CYS145
|
3.2
|
56.2
|
1.0
|
CB
|
G:CYS150
|
3.3
|
72.6
|
1.0
|
CB
|
G:HIS153
|
3.4
|
52.5
|
1.0
|
CB
|
G:HIS133
|
3.5
|
60.3
|
1.0
|
NE2
|
G:HIS133
|
4.1
|
69.1
|
1.0
|
NE2
|
G:HIS153
|
4.1
|
68.8
|
1.0
|
CD2
|
G:HIS153
|
4.1
|
63.6
|
1.0
|
CD2
|
G:HIS133
|
4.2
|
60.5
|
1.0
|
CA
|
G:HIS133
|
4.2
|
73.0
|
1.0
|
N
|
G:HIS153
|
4.3
|
59.1
|
1.0
|
CB
|
G:ALA137
|
4.3
|
81.1
|
1.0
|
CA
|
G:HIS153
|
4.5
|
63.9
|
1.0
|
CA
|
G:CYS145
|
4.6
|
66.6
|
1.0
|
CA
|
G:CYS150
|
4.7
|
72.4
|
1.0
|
O
|
G:HIS133
|
4.8
|
72.7
|
1.0
|
C
|
G:HIS133
|
4.9
|
72.9
|
1.0
|
|
Zinc binding site 9 out
of 12 in 8c61
Go back to
Zinc Binding Sites List in 8c61
Zinc binding site 9 out
of 12 in the Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 9 of Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Zn803
b:74.4
occ:1.00
|
SG
|
G:CYS166
|
2.3
|
77.0
|
1.0
|
SG
|
G:CYS169
|
2.3
|
74.8
|
1.0
|
SG
|
G:CYS225
|
2.3
|
74.1
|
1.0
|
SG
|
G:CYS229
|
2.3
|
84.2
|
1.0
|
CB
|
G:CYS229
|
3.2
|
64.7
|
1.0
|
CB
|
G:CYS166
|
3.2
|
63.9
|
1.0
|
CB
|
G:CYS225
|
3.3
|
78.6
|
1.0
|
CB
|
G:CYS169
|
3.5
|
80.1
|
1.0
|
N
|
G:CYS169
|
3.9
|
77.9
|
1.0
|
CB
|
G:ALA171
|
4.2
|
73.5
|
1.0
|
CA
|
G:CYS169
|
4.3
|
78.9
|
1.0
|
N
|
G:CYS229
|
4.3
|
85.7
|
1.0
|
CA
|
G:CYS229
|
4.3
|
89.0
|
1.0
|
CA
|
G:CYS166
|
4.7
|
75.0
|
1.0
|
CA
|
G:CYS225
|
4.7
|
72.8
|
1.0
|
CB
|
G:SER168
|
4.7
|
88.1
|
1.0
|
N
|
G:ALA171
|
4.8
|
81.8
|
1.0
|
CB
|
G:GLU231
|
4.8
|
85.0
|
1.0
|
C
|
G:CYS169
|
4.9
|
81.3
|
1.0
|
C
|
G:SER168
|
4.9
|
89.6
|
1.0
|
|
Zinc binding site 10 out
of 12 in 8c61
Go back to
Zinc Binding Sites List in 8c61
Zinc binding site 10 out
of 12 in the Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 10 of Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Zn801
b:113.3
occ:1.00
|
NE2
|
J:HIS67
|
2.1
|
112.5
|
1.0
|
SG
|
J:CYS77
|
2.3
|
122.9
|
1.0
|
SG
|
J:CYS74
|
2.3
|
118.8
|
1.0
|
SG
|
J:CYS69
|
2.3
|
125.8
|
1.0
|
CE1
|
J:HIS67
|
3.0
|
114.8
|
1.0
|
CB
|
J:CYS69
|
3.1
|
119.8
|
1.0
|
CD2
|
J:HIS67
|
3.1
|
117.4
|
1.0
|
CB
|
J:CYS74
|
3.2
|
124.2
|
1.0
|
CB
|
J:CYS77
|
3.4
|
110.7
|
1.0
|
CA
|
J:CYS69
|
3.4
|
119.2
|
1.0
|
N
|
J:CYS77
|
3.9
|
105.2
|
1.0
|
ND1
|
J:HIS67
|
4.1
|
119.3
|
1.0
|
CA
|
J:CYS77
|
4.1
|
108.0
|
1.0
|
CG
|
J:HIS67
|
4.2
|
114.6
|
1.0
|
N
|
J:MET70
|
4.4
|
123.3
|
1.0
|
C
|
J:CYS69
|
4.4
|
125.2
|
1.0
|
N
|
J:CYS69
|
4.5
|
127.3
|
1.0
|
CA
|
J:CYS74
|
4.6
|
130.5
|
1.0
|
O
|
J:GLY71
|
4.6
|
143.7
|
1.0
|
CB
|
J:PHE76
|
4.8
|
108.6
|
1.0
|
C
|
J:PHE76
|
5.0
|
110.6
|
1.0
|
O
|
J:CYS74
|
5.0
|
111.0
|
1.0
|
C
|
J:CYS74
|
5.0
|
116.3
|
1.0
|
|
Reference:
K.Wendrich,
M.Gersch.
Structure of USP54 in Complex with LYS63 Linked Diubiquitin-Pa To Be Published.
Page generated: Wed Oct 30 18:35:53 2024
|